A comprehensive collection of bioinformatics resources, focusing on single-cell RNA sequencing (scRNA-seq) and related fields. This repository organizes resources into different categories for easy access and reference.
Important
NEW: Web Admin Interface Available! We've added a visual web management tool to easily add and update resources. Run python start_web_admin.py to access the interface at http://localhost:5001. This tool features smart paper information extraction, bilingual support, and seamless integration with the existing workflow.
Research papers focusing on biological insights and discoveries using single-cell omics data.
Latest Highlights:
| Journal | Date | Title | Code | Data | Citation |
|---|---|---|---|---|---|
| Nature Network Boston | 2024 | A brain cell atlas integrating single-cell transcriptomes across human brain regions |  |
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Computational methods and tools for analyzing single-cell data.
Latest Highlights:
| Journal | Date | Title | Code | Data | Citation |
|---|---|---|---|---|---|
| Nature Communications | 2022 | Knowledge-graph-based cell-cell communication inference for spatially resolved transcriptomic data with SpaTalk | |
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Curated blog posts and articles about scRNA-seq and related topics.
| Field | Title |
|---|---|
Aging |
FIGHT AGING! |
Recommended books and learning materials.
| Field | Title |
|---|---|
Causal Inference |
A First Course in Causal Inference |
Useful databases for bioinformatics research.
| Field | Database | Description | Related paper |
|---|---|---|---|
Single-cell |
STAB | STAB2 (Spatio-Temporal Cell Atlas of Brain) provides a landscape of cell types as well as their regional heterogeneity and temporal dynamics across the human and mouse brain |
Research laboratories and groups in the field.
| Field | Lab | Masterpiece |
|---|---|---|
Bioinformatics tools |
satijalab |
Interested in contributing? We welcome contributions of all kinds:
- Add new resources through pull requests
- Report issues or suggest improvements
- Help with documentation and examples
See contribution guidelines for more details.
For information about maintaining this project, please see:
Last updated: 2025-06-21